Thirty-four eastern indigo snakes (Drymarchon couperi) naturally infected with Cryptosporidium serpentis were randomly divided into two groups. The first group received 360 mg/kg paromomycin twice weekly in a food item for 6 wk, and the second group received the food item with no treatment. Cloacal swabs were collected every 2 months for 6 months to measure C. serpentis shedding by probe hybridization quantitative polymerase chain reaction testing (qPCR). Snakes that were qPCR negative after 6 months were immunosuppressed with a single dose of 4 mg/kg dexamethasone sodium-phosphate SC. These snakes were then screened by qPCR for an additional 6 months as described above. Snakes that were qPCR negative after 1 yr of serial sampling were then re-evaluated for C. serpentis via gastric biopsy for histological and qPCR analyses. The paromomycin-treated group were significantly (P = 0.008) more likely to test qPCR negative (8/17; 47%, 95% confidence interval [CI]: 23.2–70.7) than the control snakes (1/17; 5.8%, 95% CI: 0.01–16.9) prior to immunosuppression. However, there was no significant difference (P = 0.5) in C. serpentis status following immunosuppression, as only 2/17 (11.7%, 95% CI: 0.01–26.9) paromomycin-treated snakes were qPCR negative 6 months after immunosuppression compared to 1/17 (5.8%, 95% CI: 95% CI: 0.01–16.9) control snakes. These findings suggest that 360 mg/kg paromomycin twice weekly for 6 wk in a food item is ineffective in eliminating C. serpentis in naturally infected D. couperi.